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- PDB-9lno: human Betaine/GABA transporter 1 in inward facing conformation -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9lno
Titlehuman Betaine/GABA transporter 1 in inward facing conformation
ComponentsSodium- and chloride-dependent betaine transporter
KeywordsPROTEIN TRANSPORT / transport proteins
Function / homology
Function and homology information


gamma-aminobutyric acid transport / gamma-aminobutyric acid reuptake / Reuptake of GABA / monocarboxylic acid transmembrane transporter activity / monocarboxylic acid transport / glycine betaine transport / Creatine metabolism / gamma-aminobutyric acid:sodium:chloride symporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity ...gamma-aminobutyric acid transport / gamma-aminobutyric acid reuptake / Reuptake of GABA / monocarboxylic acid transmembrane transporter activity / monocarboxylic acid transport / glycine betaine transport / Creatine metabolism / gamma-aminobutyric acid:sodium:chloride symporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / SLC-mediated transport of neurotransmitters / amino acid transport / sodium ion transmembrane transport / cell projection / presynapse / basolateral plasma membrane / membrane / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, betaine / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
CHOLESTEROL HEMISUCCINATE / Sodium- and chloride-dependent betaine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsZhao, Y. / Hao, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of transportation mechanism of hBGT1
Authors: Zhao, Y. / Xu, H.
History
DepositionJan 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium- and chloride-dependent betaine transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4254
Polymers69,4161
Non-polymers1,0093
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Sodium- and chloride-dependent betaine transporter / BGT-1 / Na(+)/Cl(-) betaine/GABA transporter / Solute carrier family 6 member 12


Mass: 69415.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A12, BGT1 / Production host: Homo sapiens (human) / References: UniProt: P48065
#2: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: structure of BGT1 protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI MORGAGNI
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1160GATAN K3 (6k x 4k)
21
31
41
51

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Processing

EM softwareName: PHENIX / Category: model refinement
Image processing
IDImage recording-ID
11
22
33
44
55
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING ONLY
22
33
44
55
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.15FSC 0.143 CUT-OFF5157319LNOPOINT
219LNOPOINT
319LNOPOINT
419LNOPOINT
55157319LNOPOINT
619LNOPOINT
719LNOPOINT
819LNOPOINT
919LNOPOINT
1019LNOPOINT
113.155157319LNOPOINT
1219LNOPOINT
1319LNOPOINT
1419LNOPOINT
1519LNOPOINT
163.155157319LNOPOINT
1719LNOPOINT
1819LNOPOINT
1919LNOPOINT
2019LNOPOINT
213.155157319LNOPOINT
2219LNOPOINT
2319LNOPOINT
2419LNOPOINT
2519LNOPOINT
263.15FSC 0.143 CUT-OFF5157329LNOPOINT
2729LNOPOINT
2829LNOPOINT
2929LNOPOINT
3029LNOPOINT
313.155157329LNOPOINT
3229LNOPOINT
3329LNOPOINT
3429LNOPOINT
3529LNOPOINT
363.155157329LNOPOINT
3729LNOPOINT
3829LNOPOINT
3929LNOPOINT
4029LNOPOINT
413.155157329LNOPOINT
4229LNOPOINT
4329LNOPOINT
4429LNOPOINT
4529LNOPOINT
463.155157329LNOPOINT
4729LNOPOINT
4829LNOPOINT
4929LNOPOINT
5029LNOPOINT
513.15FSC 0.143 CUT-OFF5157339LNOPOINT
5239LNOPOINT
5339LNOPOINT
5439LNOPOINT
5539LNOPOINT
563.155157339LNOPOINT
5739LNOPOINT
5839LNOPOINT
5939LNOPOINT
6039LNOPOINT
613.155157339LNOPOINT
6239LNOPOINT
6339LNOPOINT
6439LNOPOINT
6539LNOPOINT
663.155157339LNOPOINT
6739LNOPOINT
6839LNOPOINT
6939LNOPOINT
7039LNOPOINT
713.155157339LNOPOINT
7239LNOPOINT
7339LNOPOINT
7439LNOPOINT
7539LNOPOINT
763.15FSC 0.143 CUT-OFF5157349LNOPOINT
7749LNOPOINT
7849LNOPOINT
7949LNOPOINT
8049LNOPOINT
813.155157349LNOPOINT
8249LNOPOINT
8349LNOPOINT
8449LNOPOINT
8549LNOPOINT
863.155157349LNOPOINT
8749LNOPOINT
8849LNOPOINT
8949LNOPOINT
9049LNOPOINT
913.155157349LNOPOINT
9249LNOPOINT
9349LNOPOINT
9449LNOPOINT
9549LNOPOINT
963.155157349LNOPOINT
9749LNOPOINT
9849LNOPOINT
9949LNOPOINT
10049LNOPOINT
1013.15FSC 0.143 CUT-OFF5157359LNOPOINT
10259LNOPOINT
10359LNOPOINT
10459LNOPOINT
10559LNOPOINT
1063.155157359LNOPOINT
10759LNOPOINT
10859LNOPOINT
10959LNOPOINT
11059LNOPOINT
1113.155157359LNOPOINT
11259LNOPOINT
11359LNOPOINT
11459LNOPOINT
11559LNOPOINT
1163.155157359LNOPOINT
11759LNOPOINT
11859LNOPOINT
11959LNOPOINT
12059LNOPOINT
1213.155157359LNOPOINT
12259LNOPOINT
12359LNOPOINT
12459LNOPOINT
12559LNOPOINT
RefinementHighest resolution: 3.15 Å

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